Collect. Czech. Chem. Commun.
2005, 70, 1756-1768
https://doi.org/10.1135/cccc20051756
Hydration Gibbs Energies of Nucleic Acid Bases Determined by Gibbs Energy Perturbation, Continuous and Hybrid Approaches
Jindřich Fanfrlík, Jaroslav Rejnek, Michal Hanus and Pavel Hobza*
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague 6, Czech Republic
Abstract
The hydration Gibbs energies of adenine, cytosine, guanine, thymine, uracil and isoguanine are determined by the molecular dynamics-thermodynamic integration method (MD-TI) and using continuous COSMO and hybrid models. The role of solvents in the COSMO model is described by permittivity and by combining the permittivity and specific hydration of single water molecules placed on the energetically most probable position in the hybrid model. The hybrid model describes hydration similarly to the COSMO model; both the continuous methods are in good agreement with the MD-TI method. Differences are small and the use of both models can be recommended.
Keywords: COSMO; Hybrid model; Hydration; Gibbs energy; Nucleobases tautomers; Purines; Pyrimidines; Thermodynamic integration; Molecular dynamics; Tautomerism.
References: 32 live references.
